Question: download/cache ensembl biomaRt data for genes and their annotations?
0
gravatar for biocyberman
19 months ago by
biocyberman640
Denmark
biocyberman640 wrote:

I am working with human and rat gene sets. From a list of ensembl gene IDs, I want to retrieve columns of attributes via biomaRt. With about 4000 genes, the process runs very slowly (30 minutes). I can save the R object and use it for next times. But is there anyway for me to download a whole package of gene annotation information with gen ontology, RFAM, PFAM, Interpro, etc? In particular, I am interested in downloading the following attitutes.

This is a snippet for what I am trying to do:

library(biomaRt)
#Example of 20 gene ids.
 ensids <- c(
'ENSRNOG00000000001', 
'ENSRNOG00000000009', 
'ENSRNOG00000000040', 
'ENSRNOG00000000055', 
'ENSRNOG00000000082', 
'ENSRNOG00000000091', 
'ENSRNOG00000000129', 
'ENSRNOG00000000137', 
'ENSRNOG00000000138', 
'ENSRNOG00000000142', 
'ENSRNOG00000000156', 
'ENSRNOG00000000187', 
'ENSRNOG00000000196', 
'ENSRNOG00000000231', 
'ENSRNOG00000000233', 
'ENSRNOG00000000239', 
'ENSRNOG00000000277', 
'ENSRNOG00000000288', 
'ENSRNOG00000000307', 
'ENSRNOG00000000321')

m <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "rnorvegicus_gene_ensembl")

enstable <- getBM(mart = m, attributes = c('ensembl_gene_id','gene_biotype',
                                       'external_gene_name', 'superfamily',
                                       'family', 'go_id','goslim_goa_accession',
                                       'rfam', 'pirsf','interpro','tigrfam'),
              filters = c('ensembl_gene_id'), values = ensids)

Even though the first time download may take more time, but I see much greater benefits of subsequent uses: leave the ensembl server unstressed with repeated queries, shorter runtime, and internet independent.

biomart ensembl • 416 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by biocyberman640
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1092 users visited in the last hour